LAMMPS (3 Nov 2022)
# electrodes with thermopotentiostat
# for graphene-ionic liquid supercapacitor

boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"

atom_style full
pair_style lj/cut/coul/long 16
bond_style harmonic
angle_style harmonic
kspace_style pppm/electrode 1e-7
# kspace_modify in main script because ffield is periodic

read_data "data.graph-il"
Reading data file ...
  orthogonal box = (0 0 -68) to (32.2 34.4 68)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  3776 atoms
  scanning bonds ...
  2 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  640 bonds
  reading angles ...
  320 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     2 = max # of 1-2 neighbors
     1 = max # of 1-3 neighbors
     1 = max # of 1-4 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.021 seconds

# replicate 4 4 1 # test different sys sizes

variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top
group bot subtract ele top
416 atoms in group bot

group bmi type 1 2 3
960 atoms in group bmi
group electrolyte type 1 2 3 4
1280 atoms in group electrolyte

fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
       0 = # of size 2 clusters
       0 = # of size 3 clusters
       0 = # of size 4 clusters
     320 = # of frozen angles
  find clusters CPU = 0.001 seconds

variable q atom q
compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q
compute ctemp electrolyte temp
kspace_modify slab 3.0

unfix nvt # remove NVT thermostat included from "settings.mod"
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
832 atoms in group conp_group
# to compare to regular constant potential, switch previous line to this:
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
fix nve electrolyte nve

# note ionic liquid does not reach 500K immediately
# because its thermal response time is finite
# run this about 10k steps (10ps) to reach preset temperature
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- kspace_style pppm/electrode command:

@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:

@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM/electrode initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.20904498
  grid = 32 32 200
  stencil order = 5
  estimated absolute RMS force accuracy = 3.7023506e-05
  estimated relative force accuracy = 1.1149519e-07
  using double precision MKL FFT
  3d grid and FFT values/proc = 307242 204800
Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
  binsize = 9, bins = 4 4 16
  3 neighbor lists, perpetual/occasional/extra = 2 1 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix electrode/thermo, occasional, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) fix electrode/thermo, perpetual, skip from (1)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
   Step          Temp         c_ctemp         E_pair         TotEng         c_qbot         c_qtop    
         0   0              0              25137188       25137188       0.12767608    -0.12767608   
        50   16.63971       59.94807       25137031       25137202       0.11714711    -0.11714711   
       100   40.785523      146.93846      25136782       25137202       0.12783578    -0.12783578   
       150   53.394067      192.3634       25136653       25137203       0.080257127   -0.080257127  
       200   56.419019      203.26143      25136623       25137204       0.024756474   -0.024756474  
       250   54.922935      197.87147      25136641       25137206      -0.024533734    0.024533734  
       300   52.884861      190.52888      25136664       25137209      -0.066341109    0.066341109  
       350   52.41676       188.84244      25136670       25137210      -0.089546266    0.089546266  
       400   54.366979      195.86852      25136651       25137211      -0.10239755     0.10239755   
       450   54.906542      197.81241      25136645       25137210      -0.099987411    0.099987411  
       500   54.33841       195.7656       25136656       25137216      -0.21295943     0.21295943   
Loop time of 87.5281 on 1 procs for 500 steps with 3776 atoms

Performance: 0.494 ns/day, 48.627 hours/ns, 5.712 timesteps/s, 21.570 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 18.819     | 18.819     | 18.819     |   0.0 | 21.50
Bond    | 0.0014336  | 0.0014336  | 0.0014336  |   0.0 |  0.00
Kspace  | 34.891     | 34.891     | 34.891     |   0.0 | 39.86
Neigh   | 0.21542    | 0.21542    | 0.21542    |   0.0 |  0.25
Comm    | 0.063383   | 0.063383   | 0.063383   |   0.0 |  0.07
Output  | 0.0020476  | 0.0020476  | 0.0020476  |   0.0 |  0.00
Modify  | 33.507     | 33.507     | 33.507     |   0.0 | 38.28
Other   |            | 0.0281     |            |       |  0.03

Nlocal:           3776 ave        3776 max        3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          12504 ave       12504 max       12504 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1.72597e+06 ave 1.72597e+06 max 1.72597e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1725966
Ave neighs/atom = 457.08845
Ave special neighs/atom = 0.50847458
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:01:44
